Buggy code:
public static int fieldNum ( String name , EffFormatVersion formatVersion ) { } public static String infoFieldName ( EffFormatVersion formatVersion ) { } public static HashMap < String , Integer > mapAnn2Num ( EffFormatVersion formatVersion ) { } public static HashMap < String , Integer > mapEff2Num ( EffFormatVersion formatVersion ) { } public static String vcfEffSafe ( String str ) { } public VcfEffect ( String effectString ) { } public VcfEffect ( String effectString , EffFormatVersion formatVersion ) { } public VcfEffect ( VariantEffect variantEffect , EffFormatVersion formatVersion ) { } public VcfEffect ( VariantEffect variantEffect , EffFormatVersion formatVersion , boolean useSequenceOntology ) { } void add ( StringBuilder sb , Object obj ) { } public void addEffectType ( EffectType effectType ) { } String createAnnField ( ) { } String createEffField ( ) { } String createInfoField ( ) { } public EffFormatVersion formatVersion ( ) { } protected EffFormatVersion formatVersion ( String effectString ) { } public String getAa ( ) { } public int getAaLen ( ) { } public int getAaPos ( ) { } public String getAllele ( ) { } public String getBioType ( ) { } public int getcDnaLen ( ) { } public int getcDnaPos ( ) { } public int getCdsLen ( ) { } public int getCdsPos ( ) { } public Coding getCoding ( ) { } public String getCodon ( ) { } public int getDistance ( ) { } public String getEffectDetails ( ) { } public String getEffectsStr ( ) { } public String getEffectsStrSo ( ) { } public EffectType getEffectType ( ) { } public List < EffectType > getEffectTypes ( ) { } public String getEffectTypesStr ( ) { } public String getEffString ( ) { } public String getErrorsWarning ( ) { } public String getExonId ( ) { } public String getFeatureId ( ) { } public String getFeatureType ( ) { } public EffFormatVersion getFormatVersion ( ) { } public FunctionalClass getFunClass ( ) { } public String getGeneId ( ) { } public String getGeneName ( ) { } public String getGenotype ( ) { } public String getHgvsC ( ) { } public String getHgvsDna ( ) { } public String getHgvsP ( ) { } public String getHgvsProt ( ) { } public EffectImpact getImpact ( ) { } public int getRank ( ) { } public int getRankMax ( ) { } public String getTranscriptId ( ) { } public String getVcfFieldString ( ) { } public String getVcfFieldString ( int index ) { } public boolean hasEffectType ( EffectType effType ) { } void init ( ) { } void parse ( ) { } void parseAnn ( ) { } void parseEff ( ) { } List < EffectType > parseEffect ( String eff ) { } String parseEffectDetails ( String eff ) { } Tuple < Integer , Integer > parseSlash ( String str ) { } void set ( VariantEffect variantEffect ) { Variant var = variantEffect . getVariant ( ) ; Gene g = variantEffect . getGene ( ) ; Marker marker = variantEffect . getMarker ( ) ; Transcript tr = variantEffect . getTranscript ( ) ; if ( ! ( var . isVariant ( ) ) ) genotype = "" ; else if ( var . isNonRef ( ) ) genotype = var . getGenotype ( ) ; else genotype = var . getAlt ( ) ; effectType = variantEffect . getEffectType ( ) ; effectTypes = variantEffect . getEffectTypes ( ) ; if ( formatVersion . isAnn ( ) ) { <START_BUG> effectTypesStr = variantEffect . getEffectTypeString ( true , formatVersion . separator ( ) ) ; <END_BUG> } else { effectTypesStr = variantEffect . effect ( true , false , false , useSequenceOntology ) ; } impact = variantEffect . getEffectImpact ( ) ; funClass = variantEffect . getFunctionalClass ( ) ; if ( g != null ) { geneName = g . getGeneName ( ) ; geneId = g . getId ( ) ; } else if ( marker instanceof Intergenic ) { geneName = ( ( Intergenic ) ( marker ) ) . getName ( ) ; geneId = marker . getId ( ) ; } else { geneName = geneId = "" ; } featureType = featureId = "" ; if ( marker != null ) { if ( marker instanceof Custom ) { featureType = ( ( marker . getType ( ) ) + ( formatVersion . separator ( ) ) ) + ( ( ( Custom ) ( marker ) ) . getLabel ( ) ) ; featureId = marker . getId ( ) ; } else if ( marker instanceof Regulation ) { Regulation reg = ( ( Regulation ) ( marker ) ) ; featureType = ( ( ( ( reg . getType ( ) ) + ( formatVersion . separator ( ) ) ) + ( reg . getName ( ) ) ) + ":" ) + ( reg . getCellType ( ) ) ; featureId = marker . getId ( ) ; } else if ( marker instanceof NextProt ) { featureType = marker . getId ( ) ; featureId = ( ( NextProt ) ( marker ) ) . getTranscriptId ( ) ; } else if ( marker instanceof Motif ) { Motif motif = ( ( Motif ) ( marker ) ) ; featureType = motif . getPwmName ( ) ; featureId = motif . getPwmId ( ) ; } else if ( tr != null ) { featureType = "transcript" ; featureId = transcriptId = tr . getId ( ) ; } else { featureType = marker . getType ( ) . toSequenceOntology ( formatVersion ) ; featureId = marker . getId ( ) ; } }

Fix:
effectTypesStr = variantEffect . getEffectTypeString ( true , formatVersion ) ;